April 2018 - galaxy-commits - lists.galaxyproject.org

[galaxyproject/usegalaxy-playbook] a62d49: Use multi-manager swarm connection on Test
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a62d49033c11667e011e2e7f97f6ddddf1ef3421 https://github.com/galaxyproject/usegalaxy-playbook/commit/a62d49033c11667e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Use multi-manager swarm connection on Test Commit: 4c873738f6240db2728fed8abdcdd45c98c63558 https://github.com/galaxyproject/usegalaxy-playbook/commit/4c873738f6240db2… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/main/group_vars/galaxyservers/vars.yml M env/test/group_vars/galaxyservers/vars.yml Log Message: ----------- Log to local statsd (telegraf) rather than a centralized one, so that differences between instances can be determined Compare: https://github.com/galaxyproject/usegalaxy-playbook/compare/b3f87bde2a98...…

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[galaxyproject/usegalaxy-playbook] b3f87b: update TTS
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b3f87bde2a98d7c97c55b6effc2069aed4894bec https://github.com/galaxyproject/usegalaxy-playbook/commit/b3f87bde2a98d7c9… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M env/testtoolshed/group_vars/toolshedservers/vars.yml Log Message: ----------- update TTS

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[galaxyproject/galaxy] 2fe757: Fix for running jobs in containers.
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2fe7579d12c352b878bd9a9f3751ce7db1fb2bba https://github.com/galaxyproject/galaxy/commit/2fe7579d12c352b878bd9a9f3751… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Fix for running jobs in containers. Broken with 5861. Commit: 9e3cc281564a2f3cb91ae5c10b3ad501230228ae https://github.com/galaxyproject/galaxy/commit/9e3cc281564a2f3cb91ae5c10b3a… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/containers/docker_model.py M lib/galaxy/tools/deps/containers.py Log Message: ----------- Merge pull request #5938 from jmchilton/docker_fix_containers_lib Fix for running jobs in containers. Compare: https://github.com/galaxyproject/galaxy/compare/5acb2dff792f...9e3cc281564a

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[galaxyproject/galaxy] e6d752: Fix for running in containers when job_tmp is set ...
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: e6d752c85930bde846eb57e26de8a8716bf92b08 https://github.com/galaxyproject/galaxy/commit/e6d752c85930bde846eb57e26de8… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Fix for running in containers when job_tmp is set in job_conf.xml. Commit: 5acb2dff792fbb799215537335425b820bd16d4d https://github.com/galaxyproject/galaxy/commit/5acb2dff792fbb79921553733542… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M lib/galaxy/tools/deps/containers.py M lib/galaxy/tools/deps/docker_util.py Log Message: ----------- Merge pull request #5937 from jmchilton/docker_fix_tmp Fix for running in containers when job_tmp is set in job_conf.xml. Compare: https://github.com/galaxyproject/galaxy/compare/284795b94f2f...5acb2dff792f

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[galaxyproject/galaxy] 3182df: correct signal num
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 3182dfa70e4220621fe5eb85a05b2f5430a31d3d https://github.com/galaxyproject/galaxy/commit/3182dfa70e4220621fe5eb85a05b… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- correct signal num Commit: c85f07cf5fa2452122487cb66c3955fc88c6ea45 https://github.com/galaxyproject/galaxy/commit/c85f07cf5fa2452122487cb66c39… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/scaling.md Log Message: ----------- Merge pull request #5921 from erasche/fix-docs [18.01] correct signal num in docs Commit: fe0a4853b96ddc163ebfb09f961885b88c5577dd https://github.com/galaxyproject/galaxy/commit/fe0a4853b96ddc163ebfb09f9618… Author: E Rasche <hxr(a)hx42.org> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- forgot to document github bug reporter Commit: 393f055a2307f090f71dc2c7750b8487cfafcd96 https://github.com/galaxyproject/galaxy/commit/393f055a2307f090f71dc2c7750b… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst Log Message: ----------- Merge pull request #5928 from erasche/document-gh-reporter [18.01] forgot to document github bug reporter Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Commit: 284795b94f2fa7f2a9ad4dc82990195815de1e9c https://github.com/galaxyproject/galaxy/commit/284795b94f2fa7f2a9ad4dc82990… Author: Nicola Soranzo <nicola.soranzo(a)earlham.ac.uk> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M doc/source/admin/special_topics/bug_reports.rst M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge branch 'release_18.01' into dev Compare: https://github.com/galaxyproject/galaxy/compare/feb3e5688dd6...284795b94f2f

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[galaxyproject/galaxy] 0c321c: removed config.ini parameter from cleanup scripts
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/release_18.01 Home: https://github.com/galaxyproject/galaxy Commit: 0c321cb86e8b8658de00169a1e1e675d547efe07 https://github.com/galaxyproject/galaxy/commit/0c321cb86e8b8658de00169a1e1e… Author: Matthias Bernt <m.bernt(a)ufz.de> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- removed config.ini parameter from cleanup scripts fixes https://github.com/galaxyproject/galaxy/issues/5941 Commit: 2d772d74b940f67f48e46f21270db0362a93276c https://github.com/galaxyproject/galaxy/commit/2d772d74b940f67f48e46f21270d… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M scripts/cleanup_datasets/delete_datasets.sh M scripts/cleanup_datasets/delete_userless_histories.sh M scripts/cleanup_datasets/purge_datasets.sh M scripts/cleanup_datasets/purge_folders.sh M scripts/cleanup_datasets/purge_histories.sh M scripts/cleanup_datasets/purge_libraries.sh Log Message: ----------- Merge pull request #5956 from bernt-matthias/topic/cleanup_for18.01 removed config.ini parameter from cleanup scripts Compare: https://github.com/galaxyproject/galaxy/compare/393f055a2307...2d772d74b940

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[galaxyproject/galaxy] 2dfb48: Fix bug with remove workflow outputs from a node.
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 2dfb4875bba0059a4b44bd77e7fadb7adf6af7d7 https://github.com/galaxyproject/galaxy/commit/2dfb4875bba0059a4b44bd77e7fa… Author: John Chilton <jmchilton(a)gmail.com> Date: 2018-04-19 (Thu, 19 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Fix bug with remove workflow outputs from a node. Fixes https://github.com/galaxyproject/galaxy/issues/5931. Commit: feb3e5688dd6d97402a201e77e0179ac6dc30670 https://github.com/galaxyproject/galaxy/commit/feb3e5688dd6d97402a201e77e01… Author: Dannon <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/mvc/workflow/workflow-node.js Log Message: ----------- Merge pull request #5935 from jmchilton/workflow_outputs_fix Fix bug with removing workflow outputs from a node. Compare: https://github.com/galaxyproject/galaxy/compare/5c3e6648519d...feb3e5688dd6

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[galaxyproject/ansible-galaxy] a8a01b: code block was supposed to end
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: a8a01bb5fe0d9a5ecbf72cd6b162b719c4428ff3 https://github.com/galaxyproject/ansible-galaxy/commit/a8a01bb5fe0d9a5ecbf7… Author: E. Rasche <hxr(a)hx42.org> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M README.md Log Message: ----------- code block was supposed to end

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[galaxyproject/galaxy] 89ff88: Improve dropdown click and highlighting behavior
by GitHub 23 Apr '18

23 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: 89ff880bcde0916c6ea3ae70fabb0e4366b3fdd0 https://github.com/galaxyproject/galaxy/commit/89ff880bcde0916c6ea3ae70fabb… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-20 (Fri, 20 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Improve dropdown click and highlighting behavior Commit: 0881547bfcc0be8fbe101885543303c152103265 https://github.com/galaxyproject/galaxy/commit/0881547bfcc0be8fbe1018855433… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/style/scss/base.scss M static/style/blue/base.css Log Message: ----------- Merge remote-tracking branch 'guerler/fix_drop_selection' into dev Commit: 5c3e6648519d6591bcf3e71b6d2b4e1ba2fe1170 https://github.com/galaxyproject/galaxy/commit/5c3e6648519d6591bcf3e71b6d2b… Author: Dannon Baker <dannon.baker(a)gmail.com> Date: 2018-04-23 (Mon, 23 Apr 2018) Changed paths: M client/galaxy/scripts/apps/analysis.js M client/galaxy/scripts/components/RuleCollectionBuilder.vue M client/galaxy/scripts/components/WorkflowImport.vue M client/galaxy/scripts/mvc/tool/tool-form-composite.js M client/galaxy/scripts/mvc/upload/collection/rules-input-view.js M client/galaxy/scripts/mvc/user/user-quotameter.js M client/yarn.lock Log Message: ----------- Client format after merges. Compare: https://github.com/galaxyproject/galaxy/compare/e40c61b9a740...5c3e6648519d

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[galaxyproject/galaxy] df292f: Fix trackster links
by GitHub 21 Apr '18

21 Apr '18

Branch: refs/heads/dev Home: https://github.com/galaxyproject/galaxy Commit: df292fbf0e8c3246ec518a58385ea5a1233f0d45 https://github.com/galaxyproject/galaxy/commit/df292fbf0e8c3246ec518a58385e… Author: guerler <aysam.guerler(a)gmail.com> Date: 2018-04-18 (Wed, 18 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Fix trackster links Commit: e40c61b9a740974f3784b2cef90d1f973dabed52 https://github.com/galaxyproject/galaxy/commit/e40c61b9a740974f3784b2cef90d… Author: Martin Cech <marten(a)bx.psu.edu> Date: 2018-04-21 (Sat, 21 Apr 2018) Changed paths: M client/galaxy/scripts/viz/trackster.js Log Message: ----------- Merge pull request #5916 from guerler/fix_trackster_link Fix trackster links Compare: https://github.com/galaxyproject/galaxy/compare/d51812b832db...e40c61b9a740

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